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- PDB-2d6c: Crystal structure of myoglobin reconstituted with iron porphycene -

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Basic information

Entry
Database: PDB / ID: 2d6c
TitleCrystal structure of myoglobin reconstituted with iron porphycene
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / MYOGLOBIN / HEMOPROTEIN / PORPHYCENE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PORPHYCENE CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHayashi, T. / Murata, D. / Makino, M. / Sugimoto, H. / Matsuo, T. / Sato, H. / Shiro, Y. / Hisaeda, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Inorg.Chem. / Year: 2006
Title: Crystal structure and peroxidase activity of myoglobin reconstituted with iron porphycene
Authors: Hayashi, T. / Murata, D. / Makino, M. / Sugimoto, H. / Matsuo, T. / Sato, H. / Shiro, Y. / Hisaeda, Y.
History
DepositionNov 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8496
Polymers34,4702
Non-polymers1,3794
Water4,053225
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9253
Polymers17,2351
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9253
Polymers17,2351
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.533, 79.902, 54.619
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Myoglobin /


Mass: 17234.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: Skeletal Muscle / References: UniProt: P02185
#2: Chemical ChemComp-HME / PORPHYCENE CONTAINING FE


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.0M ammonium sulfate, 0.1M Imidazole pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2004 / Details: SI(III) MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 15759 / Num. obs: 15759 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 34.7 Å2 / Rsym value: 0.071 / Net I/σ(I): 12.5
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.93 / Num. unique all: 1515 / Rsym value: 0.275 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A6K

1a6k


Resolution: 2.26→19.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 658343.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 795 5.1 %RANDOM
Rwork0.251 ---
obs0.251 15728 97.6 %-
all-15759 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.6565 Å2 / ksol: 0.356435 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.31 Å20 Å2-6.93 Å2
2--4.03 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.26→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 96 225 2756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it5.181.5
X-RAY DIFFRACTIONc_mcangle_it6.512
X-RAY DIFFRACTIONc_scbond_it7.192
X-RAY DIFFRACTIONc_scangle_it8.792.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 116 4.8 %
Rwork0.294 2307 -
obs-2307 90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ppc.paramppc.top
X-RAY DIFFRACTION4ion.paramion.top

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